Screening of differentially expressed genes in colorectal cancer using human whole genomic oligonucleotide microarrays

Abstract

Abstract: Objective To screen the differentially expressed genes in human colorectal cancer (CRC) tissue. Methods Affymetrix oligonucleotide microarrays HG-U133 representing 32 264 human genes including 19 308 known genes and 12 956 expressed sequence tags (ESTs) were used to detect the gene expressions of CRC tissue paired with normal mucosa tissue. The microarray findings were confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction (FQ-PCR). The gene expression profiles were analyzed by intersection and complement, rank sum test and t test. Results Totally 3 125 genes and ESTs expressed differentially were detected in normal and cancer tissues, consisting of 974 up-regulated and 2 151 down-regulated genes with 247 ESTs present in CRC tissue and absent in normal mucosa and 162 ESTs absent in CRC tissue but present in normal mucosa. A percent of 80.1% of the differentially expressed genes were not reported in the literatures. Conclusion The strategy of data mining provides a foundation for filtering molecular markers and interpreting molecular carcinogenesis of CRC.

CLC Number:

R735.34

XU Hong-min¹, WANG Qiang², BAI Xue-juan², ZHONG Ding-rong³, CAO Xiu-tang⁴, ZHANG Jin-ping², Ding Yan-qing¹, YAO Kai-tai¹. Screening of differentially expressed genes in colorectal cancer using human whole genomic oligonucleotide microarrays[J]. Journal of Southern Medical University, 2005, 25(09): 1109-1113.

References

[1] Birkenkamp-Demtroder K, Christensen LL, Olesen SH, et al. Gene expression in colorectal cancer [J]. Cancer Res, 2002, 4352-63.
[2] Kwon HC, Kim SH, Rob MS. Gene expression profiling in lymph node-positive and lymph node-negative colorectal cancer [J]. Dis Colon Rectum, 2004, 47(2):141-52.
[3] 黄仲曦,丁彦青,姚开泰.用文献轮廓挖掘大肠癌转移芯片表达谱[J].第一军医大学学报,2003,23(11):1195-7.Huang ZX, Ding YQ, Yao KT. Mining microarray gene expression data of metastatic colorectal cancer by literature profiling [J].J First Mil Med Univ/Di Yi Jun Yi Da Xue Xue Bao, 2003, 23(11):1195-7.
[4] 孙青,丁彦青,高雪芹.肿瘤转移相关基因cDNA芯片的制备与应用[J].第一军医大学学报,2002,22(12):1070-6.Sun Q, Ding YQ, Gao XQ. Development and application of cDNA microarray of tumor metastasis-associated genes [J].J First Mil Med Univ/Di Yi Jun Yi Da Xue Xue Bao, 2002, 22(12):1070-6.
[5] 谷志远.现代医学分子生物学[M].北京:人民军医出版社,2000.238-9.
[6] Huang Q, Liu D, Majewski P, et al. The plasticity of dendritic cell responses to pathogens and their components[J]. Science, 2002, 26(294):870-875.
[7] Imanishi T, Itoh T, Suzuki Y, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones [J]. Plos Biol,2004, 2(6):0001-20.
[8] Zhao LP, Prentice R, Breeden L. Statistical modeling of large microarray data sets to identify stimulus-response profiles [J]. Proc Natl Acad Sci USA, 2001, 98(10):5631-6.
[9] Shou J, Soriano R, Hayward SW, et al. Expression profiling of a human cell line model of prostatic cancer reveals a direct involvement of interferon signaling in prostate tumor progression [J]. Proc Natl Acad Sci USA, 2002, 99(5):2830-5.
[10] Wood JR, Nelson VL, ho C, et al. The molecular phenotype of polycystic ovary syndrome (PCOS) theca cells and new candidate pCOS genes defined by microarray analysis [J].J Biol Chem, 2003,278(29):26380-90.
[11] LaTulippe E, Satagopan J, Smith A. Comprehensive gene expession analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease [J]. Cancer Res, 2002, 62:4499-506.
[12] Tackels-Home D, Goodman MD. Identification of differential expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling [J]. Cancer, 2001, 92(15):395-405.
[13] Jin G, Hu XG, Mao YM. Analysis of gene expression patterns in pancreatic cancer by cDNA microarray[J]. Acad J Sec Mil Med Univ. 2000, 21(9):819-22.
[14] Cousins R, Blanchard RK, Green CL, et al. A global view of the selectivity of zinc deprivation and excess on genes expressed in human THP-1 mononuclear cells[J]. Proc Natl Acad Sci USA, 2003,100(12):6952-7.